9NYT | pdb_00009nyt

Crystal structure of Human p38 alpha MAPK in Complex with MW01-32-154JS

• PDB DOI: https://doi.org/10.2210/pdb9NYT/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-28 Released: 2025-04-16 
• Deposition Author(s): Brunzelle, J.S., Shuvalova, L., Roy, S.M., Watterson, D.M.
• Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 
  0.240 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Human p38 alpha MAPK in Complex with MW01-32-154JS

Brunzelle, J.S., Shuvalova, L., Roy, S.M., Watterson, D.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.07 kDa 
• Atom Count: 2,880 
• Modeled Residue Count: 335 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	384	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539
PHAROS:  Q16539 GTEx:  ENSG00000112062

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1B7S	C [auth A]	(3P)-3-(naphthalen-2-yl)-6-(piperazin-1-yl)-4-(pyridin-4-yl)pyridazine C23 H21 N5 QUHUYHMRDJMTMH-UHFFFAOYSA-N
GG5	B [auth A], D [auth A]	4-[3-(4-FLUOROPHENYL)-1H-PYRAZOL-4-YL]PYRIDINE C14 H10 F N3 BILJSHVAAVZERY-UHFFFAOYSA-N
F50	E [auth A]	ETHANEPEROXOIC ACID C2 H4 O3 KFSLWBXXFJQRDL-UHFFFAOYSA-N
ZN	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free:  0.240 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.67	α = 90
b = 74.256	β = 90
c = 79.653	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Brunzelle, J.S., Shuvalova, L., Roy, S.M., Watterson, D.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	NIH AG031311 NIH AG043415

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release